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Patent Data: What You Don't Know Will Cost You
  Did you miss the recent class entitled Patent Data: What You Don't Know Will Cost You ? If so, you can catch up by watching the videorecording .
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—Databases  
 
—Tools
Tools to help bioresearchers write programs to data mine their data more efficiently.
Programming accelerators 
Perl packages for biological data analysis BioPerl: Perl packages for biological data analysis and manipulation        
Programmatic genome analysis environment Galaxy: programmatic analysis without programming        
Excellent language for bioanalysis Perl: when you need to learning programming fast        
Collection of small Perl scripts for bioanalysis Scriptome: learn Perl by example        
Databasing 
Excellent free SQL query editor Oracle SQL Developer, for writing relational database queries   Resource requires free Oracle Technology Network account - click here to get one    
Essential language for database querying SQL, for querying relational databases such as MySQL        
Visualization 
Free, simple visualization toolkit Google Chart API, for generating graphs quickly        
Free, advanced data analysis and visualization toolkit RapidMiner: simplified yet advanced visualization & analysis        
Flexible, easy BLAST alignment viewer BOV: BLAST alignment viewer        

Bioresearch Notifications

Solution biotool: MeV

Need to analyze microarray data? If so, have look at the MultiExperiment Viewer (MeV) from TIGR - by far the easiest way compare and visualize results generated by multiple algorithms.

So What? Success Tip #10

So What? Tip The universe of chemical compounds is enormous, complex, and frequently under-used by biologists. So what? Well, if you've ever wondered whether...

  • a compound is known to interact with your gene/protein of interest
  • whether an analog is available
  • where to buy that compound your experiment depends on
You can now quickly answer such questions from DiscoveryGate - and all Web-based too! [more]

Find Biotools

Search BioWareDB BiowareDB is a search engine for biosoftware and databases

  Browse Biodatabases:
  NAR database survey NAR provides a yearly listing of molecular biology databases, organized by subject area   Browse Bio web services:
  NAR web services survey NAR provides a yearly listing of molecular biology web services, organized by subject area

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portal mission

PharmGKB is a major repository of pharmacogenomic data for Homo sapiens. Its principal investigator is Stanford Professor of Bioengineering Russ B. Altman. The GO Ontologies are the principal ontologies describing the properties of genes and proteins of many organisms. One of its architects is Stanford Genetics Professor J. Michael Cherry. SMD is a major repository of microarray gene expression. The database is a joint project in the Departments of Biochemistry and Genetics at the School of Medicine, Stanford University. SOURCE is a data retrieval tool provided by the Department of Genetics at the School of Medicine, Stanford University.
[more] SGD is the main repository of genome data from Saccharomyces cerevisiae. Its principal investigator is Stanford Genetics Professor J. Michael Cherry.
[more] TGD is the main repository of genome data from Tetrahymena thermophila. Its principal investigator is Stanford Genetics Professor J. Michael Cherry. TGD is the main repository of genome data from Candida albicans. Its principal investigator is Stanford Genetics Assistant Professor Gavin Sherlock. SAM is a powerful tool for evaluating the statistical significance microarray gene expression data. The tool is provided by Stanford Professor of Statistics Robert Tibshirani. TGD is the main repository of genome data from Tetrahymena thermophila. Its principal investigator is Stanford Genetics Professor J. Michael Cherry. TAIR is the main repository of genome data from Arabidopsis thaliana. It is curated by personnel form Stanford's Department of Plant Biology. Using microarray data, BioProspector examines the upstream region of genes in the same gene expression pattern group, looking for regulatory sequence motifs. It was developed by Stanford Biochemistry Professor Douglas L. Brutlag. A powerful tool for microarray and genome data analysis, BioProspector examines the upstream region of genes in the same gene expression pattern group, looking for regulatory sequence motifs. It was developed by a team that includes a number of Stanford researchers. Using combined tiling array and comparative genomics data, CisGenome was developed by a team that includes Stanford Professor of Statistics Wing Wong. This resource is restriced to holders of a SUNet ID. StepMiner was developed by a team that includes Stanford Professor of Statistics Robert Tibshirani, Stanford Associate Professor of Radiology Sylvia K. Plevritis, and Stanford Professor of Computer Science David L. Dill.
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